Setup

Background

Datasets

Ramakar et al (2017)

##                                                        V1
## RunID                                         -0.92207331
## SampleID                                       0.56588402
## SampleACC                                      0.52187022
## ExperimentACC                                  0.52227248
## ExperimentTitle                                0.52227248
## SampleAttributes                              -0.72217656
## ExperimentAttributes                           0.52227248
## SampleName                                     0.52227248
## SampleTitle                                   -1.23951411
## SampleBases                                    1.12469750
## SampleSpots                                    1.12469750
## RunPublished                                   0.55583963
## Size                                           1.13646420
## RunTotalBases                                  1.12469750
## RunTotalSpots                                  1.12469750
## NumSpots                                       1.12469750
## ReadInfo                                       0.39151818
## RunAlias                                       0.56588402
## Percent_aligned_Chimeric                       0.01401913
## Percent_aligned_ChrX                          -1.10900870
## Percent_aligned_ChrY                          -1.22596746
## AUC_all_alignments                             1.16003963
## AUC_all_annotated_exons                        1.15464673
## AUC_uniquely_aligned                           1.15450709
## AUC_all_annotated_exons_unique                 1.15267282
## AUC)all_percentage                            -0.20375605
## AUC_unique_percentage                         -0.32956490
## Total_fragments                                1.15974100
## Read_Fragment_length                           1.16334602
## Mean_Fragment_length                          -0.74930177
## Mean_Fragment_length_BAM                      -1.44864053
## Mode_Fragment_Length                          -1.36344896
## Mode_Fragment_Length_Count                     0.98793867
## Percentage_fragment_mapped_exon_fc            -0.82778239
## Percentage_fragment_mapped_unique_exon_fc     -0.92522176
## Total_fragments_input_fc_exon_fc               1.15700790
## Total_fragments_assigned_exon_fc               1.08295864
## Total_fragments_count_unique_exon_fc           1.15700790
## Total_fragments_count_unique_assigned_exon_fc  1.08295864
## Percentage_fragment_mapped_gene_fc            -0.75947235
## Percentage_fragment_mapped_unique_gene_fc     -0.88428933
## Total_fragments_input_fc_gene_fc               1.15700790
## Total_fragments_assigned_gene_fc               1.09171621
## Total_fragments_count_unique_gene_fc           1.15700790
## Total_fragments_count_unique_assigned_gene_fc  1.08145691
## Intron_sum                                     0.71789243
## Intron_sum_percentage                         -0.89706236
## Percentage_chimeric_reads_STAR                -0.59599104
## Percentage_mapped_multi_loci_STAR             -1.08002420
## Percentage_mapped_too_many_loci_STAR          -0.82344064
## Percentage_unmapped_other_STAR                -0.57569697
## Percentage_unmapped_too_short_STAR            -1.87378200
## Total_mapped_STAR                              1.15974100
## Average_mapped_length_STAR                    -0.31376005
## Deletion_average_length_STAR                  -0.54905080
## Deteltion_rate_per_base_STAR                  -0.29299586
## Insertion_average_length_STAR                 -0.54415312
## Insertion_rate_per_base_STAR                  -1.51015141
## Mapping_speed_per_hour_STAR                   -0.95678448
## Percentage_mismatch_per_base_STAR             -1.73177086
## Number_of_chimeric_reads_STAR                  1.10762237
## Total_input_reads_STAR                         1.12469750
## Number_reads_mapped_to_multiple_loci_STAR      0.95868089
## Number_reads_mapped_to_too_many_loci_STAR      0.81135118
## Number_reads_unmapped_other_STAR               0.52753358
## Number_reads_unmapped_too_short_STAR          -0.52434834
## Number_canonical_splices_AT_AC_STAR            0.74891267
## Number_canonical_splices_GC_AG_STAR            0.77264527
## Number_canonical_splices_GT_AG_STAR            0.77206646
## Number_non_canonical_splices_STAR              1.03569281
## Number_splices_total_STAR                      0.77455521
## Total_percentage_mapped_STAR                  -0.25005180
## Percentage_uniquely_mapped_STAR                1.15417303
## Junction_count                                 0.70888310
## Junction_coverage                              0.78152832
## Junction_average_coverage                      0.69608728
## Number_input_reads_both_STAR                   1.12469750
## All_mapped_reads_both_STAR                     1.15974100
## Number_chimeric_reads_both_STAR                1.10762237
## Number_reads_mapped_multiple_loci_both_STAR    0.95868089
## Numner_reads_mapped_too_many_loci_both_STAR    0.81135118
## Number_reads_unmapped_other_both_STAR          0.52753358
## Number_reads_unmapped_too_short_both_STAR     -0.52434834
## Number_reads_mapped_uniquely_both_STAR         1.15417303
## Percentage_mapped_both_STAR                   -0.30067430
## Percent_Chimeric_both                         -0.59525170
## Percentage_mapped_multi_loci_both_STAR        -1.07919545
## Percentage_mapped_too_many_loci_both_STAR     -0.77900075
## Percentage_unmapped_other_both_STAR           -0.71156482
## Percentage_unmapped_too_short_both_STAR       -1.87393185
## Percentage_uniquely_mapped_both_STAR          -0.24988415
## DIstinctQualityValues                         -0.38163684
## Percent_Bases                                  1.12469750
## Percent_A                                      0.32372534
## Percent_C                                     -2.26309208
## Percent_G                                     -2.29141772
## Percent_T                                      0.16873923
## Percent_N                                     -1.64022797
## Average_Phred                                 -0.33017200
## ErrQ                                          -0.50054673
## SampleAccPrediction                            0.52187022
## PredictionType                                -1.85518724
## BigWigFile                                    -1.23564405
## Age                                           -0.73338606
## pH                                            -0.98860509
## StructureAcronym                              -1.05218257
## Diagnosis                                     -1.02821128
## Ethnicity                                     -0.70033387
## Sex                                           -1.28230304
## PMI                                           -1.02004084
## Regions                                       -1.07465807
## Age_rounded                                   -0.73338606
## AgeInterval                                   -0.74480077